Evidence map›Paper›PMID 25044324›Full record

ArticleProtein science : a publication of the Protein Society2014

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Abhinav Kumar, Marco Punta, Herbert L Axelrod, Debanu Das, Carol L Farr, Joanna C Grant, Hsiu-Ju Chiu, Mitchell D Miller, Penelope C Coggill, Heath E Klock and 5 more

Abstract read
In one paragraph

Article in Protein science : a publication of the Protein Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.Acta crystallographica. Section D, Structural biology · 2016
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Abhinav KumarJoint Center for Structural Genomics, http://www.jcsg.org; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025.
Marco Punta
Herbert L Axelrod
Debanu Das
Carol L Farr
Joanna C Grant
Hsiu-Ju Chiu
Mitchell D Miller
Penelope C Coggill
Heath E Klock
Marc-André Elsliger
Ashley M Deacon
Adam Godzik
Scott A Lesley
Ian A Wilson

Funding

Structure Determination Core at SSRLU54GM094586 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI WILSON, IAN A · 2010 to 2014
$40.1M
X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
NIGMS NIH HHS P41 GM103393NIGMS NIH HHS P41GM103393NIGMS NIH HHS U54 GM094586
6 · The paper itself

Abstract

Crystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight-stranded, calycin-like, β-barrel fold and bind an endogenous unknown ligand at one end of the β-barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.

Indexed as

Carbohydrate MetabolismBacterial ProteinsBacteroidesBinding SitesCrystallography, X-RayModels, MolecularMolecular Sequence DataProtein Structure, SecondarySequence AlignmentBacterial ProteinsBacteroidescalycinscrystal structureDUF4488sugar bindingunknown ligand

Identifiers

PMID25044324
PMCPMC4287006

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.